Site-specific DNA recombination is the central regulatory mechanism in many developmental pathways in prokaryotes and eukaryotes. The chemical mechanism of strand cleavage and strand transfer during site-specific recombination must have overall similarities to mechanisms of general recombination, DNA transposition and RNA splicing. We intend to study the chemical features of the strand breakage and strand joining reactions mediated by the Flp recombinase from Saccharomyces cerevisiae and other related recombinases. We wish to analyze the type of DNA-protein and protein-protein interactions that confer selectivity of phosphoryl transfer and drive strand joining in the recombinant mode. Understanding the chemistry of this reaction may help in the design of drugs that can specifically inhibit this chemistry. Such drugs could be used to prevent undesirable DNA recombination: for example, viral integration. Site- specific recombination also permits targeted integration of genetic information- the basic rationale in gene therapy.